2014 EuPathDB Workshop
2014 Schedule
The course begins at 6:30 pm on Sunday, June 15th with a reception.(If you arrive before the 4:00 pm hotel check-in time, you can call that day to see if your room is available for earlier check in. The Hotel can not guarantee your room will be ready before 4:00 pm. The number is 1-706-549-4433. There is a free hotel shuttle that can take you downtown for sightseeing while you wait.)
The course will finish at 5:00 pm on Wednesday, June 18th.
Participants will be provided with desktop computers to use in the workshop sessions. You are welcome to bring your own laptop to use in other areas. The Holiday Inn Hotel provides free high-speed Internet in all rooms and lobby.| Time | Place | Event | Instructor |
|---|---|---|---|
| Sunday, June 15th | |||
| 6:30-9:00pm | Holiday Inn Georgian Ballroom |
Registration & Welcome Reception General introduction to EuPathDB and omics Workshop attendees and instructors introductions Transportation information |
Jessie Kissinger, Omar Harb, Susanne Warrenfeltz |
| Monday, June 16th | |||
| 7:00am | Holiday Inn Redfearn Grille |
Optional Breakfast (breakfast coupons provided in welcome packet) | |
| 8:30-8:45am | Life Sciences Room C128 |
General Workshop Introduction | Eileen Kraemer, Susanne Warrenfeltz, Omar Harb |
| 8:45-9:00am | Introductory Glossary Survey | Jessica Kissinger | |
| 9:00-9:45am | Site Usability Exercise |
Eileen Kraemer, Susanne Warrenfeltz |
|
| 9:45-10:30am | Room C128 | Introduction to EuPathDB sites and the search strategy system | Omar Harb |
| 10:30-10:45am | Room B116 | Morning Coffee Break (food provided) | |
| 10:45-12:15pm | Room C128 | Exercise I: Finding genes and building search strategies |
Susanne Warrenfeltz |
| 12:15-1:15pm | Room B116 | Lunch (provided) | |
| 1:15-1:30pm | Room C128 | Glossary Survey Results |
Jessica Kissinger |
| 1:30-2:30pm | Exercise II: Viewing data on gene pages and in the Genome Browser |
Susanne Warrenfeltz | |
| 2:30-2:45pm | Introduction to High throughput sequence analysis Borodina, et al Levin, et al Zhang, et al |
Omar Harb | |
| 2:45-3:00pm | Room B116 | Afternoon Snack Break (provided) | |
| 3:00-3:45pm | Room C128 | Exercise III: RNA sequence data analysis (Part 1: using pathogen portal's RNAseq pipeline) Group Exercise |
Omar Harb, Brian Brunk |
| 3:45-4:45pm | Introduction to SNPs in EuPathDB Exercise IV: Population (SNPs) data |
Brian Brunk | |
| 4:45-5:30pm | Exercise V: Metabolic Pathways and Compounds |
Omar Harb | |
| 6:00-8:00pm | Coverdell Center Room 340 |
Dinner | |
| Tuesday, June 17th | |||
| 7:30am | Holiday Inn Redfearn Grille |
Optional Breakfast | |
| 9:00-10:00am | Life Sciences Room C128 |
Exercise VI: Protein motifs and domains RegEx Help RegEx Lecture |
Omar Harb |
| 10:00-10:30am | Exercise VII: DNA motifs |
Brian Brunk, Susanne Warrenfeltz |
|
| 10:30-10:45am | Room B116 | Morning Coffee Break | |
| 10:45-11:15am | Room C128 | Exercise VII: DNA motifs (continued) | |
| 11:15-12:15pm | Exercise VIII: Isolate data |
Jessica Kissinger | |
| 12:15-1:15pm | Room B116 | Lunch | |
| 1:15-2:15pm | Room C128 | Exercise IX: Orthology and phylogenetic profiles |
Brian Brunk |
| 2:15-2:45pm | Exercise X: Data retrieval and download |
Susanne Warrenfeltz | |
| 2:45-3:00pm | Room B116 | Afternoon Snack Break | |
| 3:00-4:00pm | Room C128 | Exercise XI: RNA sequence data analysis (Part 2: viewing and analyzing your results - continuation of exercise 3). Group Exercise |
Omar Harb, |
| 4:00-5:30pm | Room C128 | Exercise XII: Exploring proteomics data |
Brian Brunk, Susanne Warrenfeltz |
| 5:30-5:45pm | Description of Exercise XV Group Exercise | Omar Harb | |
| Wednesday, June 18th | |||
| 7:30am | Holiday Inn Redfearn Grille |
Optional Breakfast | |
| 9:00-10:30am | Life Sciences Room C128 |
Exercise XIII, Part I: Exploring transcriptomic data |
Brian Brunk, Omar Harb, Susanne Warrenfeltz |
| 10:30-10:45am | Room B116 | Morning Coffee Break | |
| 10:45-11:45pm | Room C128 | Exercise XIII, Part II: Exploring transcriptomic data | Brian Brunk, Omar Harb, Susanne Warrenfeltz |
| 11:45-12:15pm | User Feedback (new features in EuPathDB)
New Features Exercise |
Eileen Kraemer, Susanne Warrenfeltz |
|
| 12:15-1:15pm | Room B116 | Lunch | |
| 1:15-2:15pm | Exercise XIV: Complex strategy using genomic colocation |
Omar Harb, Susanne Warrenfeltz |
|
| 2:15-2:45 | Room C128 | Designing a vaccine | Omar Harb |
| 2:45-3:00pm | Room B116 | Afternoon Snack Break | |
| 3:00-4:45pm | Room C128 | Exercise XV: Complex strategy (finding vaccines and drug targets) Group Exercise |
Omar Harb |
| 4:45-5:00pm | Outreach | Omar Harb, Susanne Warrenfeltz |
|
| 5:00-5:30pm | Exit survey and general discussion | ||